Package: vulcan

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vulcan_1.6.0.tar.gz

StartedAt: 2019-10-16 07:43:11 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:51:47 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 515.6 seconds

RetCode: 0

Status:  OK

CheckDir: vulcan.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vulcan_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/vulcan.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vulcan/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vulcan’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ChIPpeakAnno', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'zoo',
  'GenomicRanges', 'S4Vectors', 'viper', 'DiffBind', 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘vulcan’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
average_fragment_length 5.951  0.443   6.428
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/vulcan.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL vulcan
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘vulcan’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vulcan)

name	user	system	elapsed
average_fragment_length	5.951	0.443	6.428
corr2p	0.002	0.001	0.002
densityauc	0.030	0.001	0.032
dpareto	0.004	0.000	0.005
fisherp	0	0	0
gsea	1.253	0.103	1.355
kmgformat	0.012	0.002	0.014
null_gsea	0.047	0.007	0.054
p2corr	0	0	0
p2z	0.000	0.000	0.001
pareto.fit	0.007	0.002	0.009
plot_gsea	0.046	0.004	0.049
ppareto	0.004	0.001	0.005
rea	0.003	0.001	0.004
slice	0.001	0.001	0.001
stouffer	0.001	0.000	0.000
textplot2	0.257	0.040	0.297
val2col	0.004	0.001	0.005
vulcan	2.983	0.252	3.238
vulcan.annotate	1.519	0.142	1.662
vulcan.import	0.029	0.003	0.032
vulcan.normalize	0.000	0.000	0.001
vulcan.pathways	1.839	0.143	1.981
wstouffer	0.000	0.000	0.001
z2p	0.001	0.000	0.000